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Biochemistry Enzymes
Random Biochemistry Test Prep Questions
51
Chemistry
10/14/2009

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Term
How is the THI stabilized during in the enzyme Chymotrypsin?
Definition
The oxyanion hole stabilizes the charge. Glycine-193 and Serine-195 donate hydrogen bonds to stabilize the negatively charged oxygen.
Term
What is DIPF and TCPK and what are their significance?
Definition
DIPF= Diisopropylphosphofluoridate and it reacts with the active site serine-195 on Chymotrypsin to elucidate it's catalytic importance. TCPK is another inhibitor of chymotrypsin that binds to the active site histine-57 to show its enzymatic importance.
Term
How was the 2 step mechanism determined for chymotrypsin?
Definition
A chromogenic substate called N-acetyl-L-phenylalanine-p-nitrophenyl ester was introduced to chymotrypsin and the absorbance of the yellow product produced was measured. The results showed an initial burst phase followed by a steady phase suggesting the second step is the rate limiting step.
Term
Name the properties of starch and glycogen:
Definition
Starch and glycogen are polysaccharides of glucose molecules. They are bound by a(1,4) linkages which cause them to adopt a helical shape. Glycogen is also highly branched with a(1,6) linkages every 8-12 residues.
Term
Why is ASP-102 so conserved in the structure of chymotrypsin?
Definition
It stabilizes the rotatable bonds on the histidine, pointing it in the optimum direction to interact with SER-195.
Term
How is Glycogen branched?
Definition
a (1,4) for linear glycosidic bonds, a (1,6) for branching bonds
Term
How are N-linked carbohydrates attached to proteins?
Definition
Theough linkage with amide nitrogen of asparginine. This always results in a core of 2-N-acetylglucosamine linked with a mannose triad.
Term
How is lactose bound?
Definition
Galactopyranosyl is bound to glucopyranose through a b(1,4) linkage.
Term
Name the four strategies that enzymes use to accomplish chemistry:
Definition
1. Covalent Catalysis, 2. General acid/base catalysis, 3. Metal Ion Catalysis, 4. Catalysis by approximation,
Term
What is the consequence of a(1,4) linkages?
Definition
It constrains the polymer to be curved creating helices.
Term
How are O-linked carbohydrates attached to proteins?
Definition
Linked to the hydroxyl group of either serine or threonine usually by N-acetylgalactosamine.
Term
How is sucrose bound?
Definition
Glucose is bound to fructose in an a(1,2) glycosidic bond.
Term
In sucrose, what is the configuration of the anomeric carbon of the fructose constituent?
Definition
Beta
Term
The larger the Kcat/Km ratio does what to the catalytic efficiency of an enzyme?
Definition
Increases catalytic efficiency.
Term
Since the peptide bond is kinetically favorable, how are enzymes able to cleave the bond?
Definition
Enzymes use 3 tools: 1. Active site uses a potent nucleophile to attack the carbonyl carbon, 2. The peptide carbonyl is further polarized to make the carbonyl carbon even more susceptible to nucleophilic attack, 3. Stabilize the intermediates in order to drive the reaction forward.
Term
What sugar contributes to a RBC being an A antigen?
Definition
N-Acetylgalactisamine
Term
What are the consequences of glycogen's branching?
Definition
The structure is highly dense and has multiple ends available for enzymatic degredation
Term
How is Maltose bound?
Definition
Glucopyranosyl is linked to glucopyranose through an a(1,4) linkage
Term
What sugar contributes to a RBC having a B antigen?
Definition
Galactose
Term
Name the properties of cellulose?
Definition
Cellulose is a polysaccharide that is made up of b(1,4) linkages between glucose molecules. The linearity allows the glucose molecules to hydrogen bond with one another in strands giving cellulose great tinsile strength.
Term
In ABC Transporters, how is the substrate transported across the membrane? What role does ATP play in this process?
Definition
ATP binds to the binding casette to create a conformational change in the transporter to release the substrate. ATP hydrolysis resets the transporter to its original state.
Term
Why is adding phosphate an effective means of regulating protein activity?
Definition
1. Its -2 charge allows for a conformational change, 2. The phosphoryl group can accept 3 or more hydrogen bonds, 3. The free energy of phosphorylation is rather high and is a good means of keeping the signal on or off, 4. The timescale that phosphorylation lasts is controlable to seconds up to hours, 5. Amplification, 6. ATP links phosphorylation to energy metabolism to signaling
Term
What is CTP and what is its significance?
Definition
CTP is an allosteric effector of aspartate transcarbamoylase and is not a substrate analog. It affects the regulatory subunit and thus affects the T/R state transition.
Term
What mechanism do NMP kinases use?
Definition
Catalysis by approximation and metal ion catalysis
Term
What is the role of the divalent cations in NMP kinases?
Definition
Mg2+ and Mn2+ have 3 roles: 1. Neutralize the negative charges of the substrate, 2. Properly position the substrate, 3. Provide additional interactions with the enzyme
Term
Name the common covalent modifications of protein activity:
Definition
1. Phosphorylation, 2. Acetylation, Myristoylation (lipidation), 3. ADP-ribosylation, 4. Farnesylation, 5. gamma-Carboxylation, 6. sulfation, 7. Ubiqitination
Term
Where does glycosylation occur?
Definition
the lumen of the ER
Term
Which amino acid residues are sugars commonly linked in glycoproteins?
Definition
Ser, Thr, Asp
Term
What are the 6 major classes of enzymes?
Definition
1. Transferase, 2. Oxidoreductase, 3. Hydrolase, 4. Lyase, 5. Isomerases, 6. ligases
Term
What do transferases do?
Definition
catalyze group transfer reactions. ex: NMP kinases
Term
What do oxidoreductases do?
Definition
Catalyze oxidation/reduction reactions. Ex: lactate dehydrogenase
Term
What do hydrolases do?
Definition
Catalyze hydrolysis reactions. Ex: chymotrypsin
Term
What do lyase reactions do?
Definition
Catalyze the addition or removal of double bonds. Ex: fumarase
Term
What do isomerases do?
Definition
Catalyze intramolecular group transfer. Ex: triose phosphate isomerase
Term
Wha do ligases do?
Definition
Join two substrates. Requires ATP.
Term
What does Keq tell us? Kcat?
Definition
Keq tells us how favoable a reaction is. Kcat tells us how fast the reaction is.
Term
What does an enzyme have the highest affinity for: the substrate, the transition state, the product?
Definition
The transition state because if it was completely complementary to either the substrate or the product, it would not catalyze a reaction and would be stuck in the ES or EP complex.
Term
How can we neglect k-2 reverse reaction in the formulation of kcat?
Definition
In early points during the reaction, we can assume that product levels are low and the reverse reaction can be neglected.
Term
What is Km defined as?
Definition
Km=(k-1+k2)/k1
Term
In a lineweaver-burke plot, what do the x and y axis' represent?
Definition
Y axis: 1/V0, X axis: 1/[S]. This means that the greater value on the Y axis, the slower the initial velocity and the greater the number on the x-axis represents the lower the concentration of the substrate.
Term
What do the y and x intercept represent on the lineweaver burke plot? The slope?
Definition
y intercept is 1/Vmax; x intercept is -1/Km; Slope= Km/Vmax
Term
What factors does Km depend on?
Definition
pH, temperature and ionic strength
Term
What does Km mean?
Definition
1. It is the concentration at which half of the active sites are filled for catalysis. 2. It tells us about the stability of the ES complex. If Km is high it tells us that the ES compex is unstable and vice-versa.
Term
Whay is Vmax?
Definition
It is the max amount of product that is formed when the enzyme is saturated.
Term
How do we measure catalytic efficiency?
Definition
kcat/Km
Term
What does kcat/Km tell us?
Definition
kcat/Km tells us about the catalytic efficiency under typical cellular concentrations. Sinc cellular concentrations rarely approach those to reach Vmax, kcat/Km tells us both about the rate of ES formation and catalytic rate. The larger this number, the better the enzyme is at performing under cellular conditions. This can also tell us the preferace toward certain substrates for a particular enzyme.
Term
What are the types of enzyme inhibition?
Definition
1. Competitive, 2. Uncompetitive, 3. Mixed, 4. Irreversible
Term
What are the characteristics of competitive inhibition?
Definition
It occcurs only at the active site. It essentially removes enzyme from the solution. Does not affect Vmax since adding more and more substrate will eventually lead to reaching Vmax. It increases the apparent Km value due to the need of more substrate.
Term
What are the features of uncompetitive inhibition?
Definition
It only binds to the ES complex away from the active site.
Term
What does a LWB plot look like of a competitively inhibited enzyme?
Definition
It changes the Km but not the Vmsx, so therefore it will change the slope to make the graph steeper with the same y-intercept.
Term
What does a LWB plot look like of an uncompetitvely inhibited enzyme?
Definition
Since both the Km and Vmax are affected, the graph is shifted up with a larger y intercept and more negative x intercept. The slope, however, is not changed.